Neanderthal DNA Is Being Purged From Our Genomes

Neanderthal gene variants are disappearing from modern populations and the slow purge is inevitable.

Another Neanderthal extinction is taking place now, and it's happening in our genomes, suggests new research that finds natural selection is slowly removing Neanderthal genetic variants from modern populations.

Our ancestors interbred with Neanderthals when they migrated out of Africa, yet people of European and Asian ancestry today are only about 1 to 4 percent Neanderthal, according to most estimates. The new study, published in PLOS Genetics, helps explain what happened to all of those other Neanderthal gene signatures that were more evident right after our species - known as anatomically modern humans, or AMH - mated with Neanderthals.

"So the first generation of hybrids would have been half Neanderthal and half AMH because they had one Neanderthal parent and one AMH parent," senior author Graham Coop, a professor in the UC Davis Department of Evolution and Ecology and Center for Population Biology, told Seeker.

"Later generations of hybrids may have more or less Neanderthal ancestry," he continued, "depending on whether they had more Neanderthal or AMH ancestors (e.g. great grandparents)."

Coop said they're finding that the early Neanderthal-human mixes seem to have inherited mostly weak gene variants from their Neanderthal parents.

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To understand the phenomenon, we need to go further back in time. It is widely believed that the ancestors of Neanderthals split from our African ancestors over half a million years ago. Because there was a longstanding connection before then, we share the majority of our genome with Neanderthals. This DNA is not described as being Neanderthal, however, as the Neanderthals only started to evolve as a unique population after the split with AMH occurred.

Once in Europe and Asia, the Neanderthals evolved genetic variants in response to their living conditions. It's believed that they existed in small, isolated populations, given the often chilly climate and what resources were available to them.

Another migration occurred around 50,000–80,000 years ago, when AMH left Africa and spread through Europe and Asia, encountering and interbreeding with Neanderthals. The nature of those encounters remains a mystery, but DNA evidence show they happened.

Some of the genetic variants inherited from Neanderthals are beneficial. People from Tibet, for example, can breathe easier in high elevations thanks to their Neanderthal heritage. Other Neanderthal genetic variants, however, are not so great.

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"Small, long isolated populations are relatively more inbred than large populations," Coop explained, adding that such groups can accumulate gene variants that aren't very helpful to our survival. This is the DNA that is gradually disappearing from the genomes of people with European and Asian heritage.

Coop and his team devised methods to measure the degree of natural selection acting on Neanderthal DNA, and were able to show how this purging is happening slowly over time.

Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology, previously told Seeker "that there are regions of the modern human genomes where we would statistically expect to see a contribution from Neanderthals but do not. So in some regions of the modern human genome there seem to be selection against a Neanderthal contribution."

Pääbo says that genes expressed in male testicles in particular suggest that hybrid individuals may have had some problems with male fertility.

The new research focuses on Neanderthals, but AMH likely interbred with other populations of humans, both in and outside of Africa. Coop believes his findings could also help explain what's causing the gradual disappearance of Denisovan genetic variants from the genomes of Melanesians, Aboriginal Australians and certain other people living today.

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